As after half a year there is still no answer, here are some very short answers from my comments:
the difference is just the file ending as far as I know.
if you have installed MATLAB (or another software which also uses .m file extension) it is easier to let the OS distinguish between MATLAB files and Mathematica packages.
because that now seems to be the extension preferred by WRI, most probably more for marketing reasons than because of answer 2. My impression is that .m was just left to work for compatibility reasons, but maybe I'm wrong with that...
Despite answer 1. there is obviously a new problem when Mathematica needs to load a package and there are both a .m and a .wl file with the same name. It seems that there are differences in the order in which package files are loaded and that has seen some changes at least in early 10.x versions (check the Wolfram Groups discussion mentioned in your question). But that will probably only be relevant when you mix old (.m) and new (.wl) conventions which is something you obviously should avoid.
One more difference is the support within the Workbench which still doesn't know about .wl files. But maybe I just don't know how to get the most recent version, does anyone know what the newest is? The update site announces 2.0.138 to be the newest for years (still true in June 2016)...